One other possible cause became apparent to me a several days ago when h.264 decoding became very bad after replacing a bad power supply. Up until then Ubuntu 9.10 seemed to have only marginally less performance under VLC for this than the Windows 2k I have abandoned.
I had set the multiplier in the BIOS from AUTO to a mis-remembered, too low multiplier. Setting the CPU multiplier in my BIOS from AUTO to the correct multiplier has brought the apparent performance up to the Windows level. Ubuntu now whines at me after rebooting that "Frequency Scaling is Unsupported," but I ignore it.
I think Ubuntu may be capable on some motherboards of adjusting the clock multiplier with CPU load, but whatever it does is not sufficient to get h.264 decoding to operate at full performance on mine. Forcing the full (not-overclocked) multiplier fixed it.
kirby
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